Using RecoBundles for bundle recognition#

For bundle recognition, pyAFQ defaults to use the waypoint ROI approach described in [Yeatman2012]. However, as an alternative approach, pyAFQ also supports using the RecoBundles algorithm [Garyfallidis2017], which uses an atlas of bundles in streamlines. This example shows how to use RecoBundles for bundle recognition.

The code closely resembles the code used in sphx_glr_tutorial_examples_plot_001-plot_afq_api.py.

import os.path as op
import AFQ.data.fetch as afd
from AFQ.api.group import GroupAFQ
import AFQ.api.bundle_dict as abd

afd.organize_stanford_data(clear_previous_afq="track")

tracking_params = dict(n_seeds=25000,
                       random_seeds=True,
                       rng_seed=42)

Defining the segmentation params#

We also refer to bundle recognition as the “segmentation” of the tractogram. Parameters of this process are set through a dictionary input to the segmentation_params argument of the GroupAFQ object. In this case, we use abd.reco_bd(16), which tells pyAFQ to use the RecoBundles algorithm for bundle recognition.

myafq = GroupAFQ(
    output_dir=op.join(afd.afq_home, 'stanford_hardi', 'derivatives',
                       'recobundles'),
    bids_path=op.join(afd.afq_home, 'stanford_hardi'),
    # Set the algorithm to use RecoBundles for bundle recognition:
    bundle_info=abd.reco_bd(16),
    preproc_pipeline='vistasoft',
    tracking_params=tracking_params,
    viz_backend_spec='plotly_no_gif')

fig_files = myafq.export_all()
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100%|██████████| 179864/179864.0 [00:38<00:00, 4659.42it/s]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]
Optimizing level 2 [max iter: 10000]
Optimizing level 1 [max iter: 1000]
Optimizing level 0 [max iter: 100]

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/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/site-packages/AFQ/recognition/utils.py:92: UserWarning:

Streamlines do not have the same number of points. All streamlines need to have the same number of points. Use dipy.tracking.streamline.set_number_of_points to adjust your streamlines


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References:#

Garyfallidis2017

Garyfallidis, Eleftherios, Marc-Alexandre Côté, Francois Rheault, Jasmeen Sidhu, Janice Hau, Laurent Petit, David Fortin, Stephen Cunanne, and Maxime Descoteaux. 2017.“Recognition of White Matter Bundles Using Local and Global Streamline-Based Registration and Clustering.”NeuroImage 170: 283-295.

Total running time of the script: (15 minutes 41.235 seconds)

Estimated memory usage: 2537 MB

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